PyComplexHeatmap: a Python package to visualize multimodal genomics data

Python has emerged as a robust programming language increasingly employed in genomics data analysis, largely due to its comprehensive deep learning libraries and proficiency in handling large-scale data, such as single-cell multi-omics datasets. Although Python has become a prominent data science ecosystem for bioinformatics, there remains a growing demand for advanced heatmap visualization and assembly tools, which are not sufficiently addressed by existing Python-based data visualization libraries. We present PyComplexHeatmap, an all-inclusive Python library for heatmap visualization, inspired by the ComplexHeatmap package currently available in R. PyComplexHeatmap is built upon the matplotlib library and features a versatile, modular interface that seamlessly integrates with other Python-based data science tools, such as Pandas, NumPy, and genomics tools, such as Scanpy, in a standard-compliant manner. This library caters to the requirements of exquisite rendering of multimodal matrix data, incorporating both textual and graphical annotations, thereby enabling efficient integrative analysis of multimodal data and associated metadata.